velvet_1.2.03~nozlibcopy-1_amd64.deb


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Description

velvet - Nucleic acid sequence assembler for very short reads

Property Value
Distribution Debian 7 (Wheezy)
Repository Debian Main amd64
Package name velvet
Package version 1.2.03~nozlibcopy
Package release 1
Package architecture amd64
Package type deb
Installed size 2.06 KB
Download size 674.88 KB
Official Mirror ftp.br.debian.org
Velvet is a de novo genomic assembler specially designed for short read
sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and
Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near
Cambridge, in the United Kingdom.
Velvet currently takes in short read sequences, removes errors then produces
high quality unique contigs. It then uses paired read information, if
available, to retrieve the repeated areas between contigs.

Alternatives

Package Version Architecture Repository
velvet_1.2.03~nozlibcopy-1_i386.deb 1.2.03~nozlibcopy i386 Debian Main
velvet - - -

Requires

Name Value
dpkg >= 1.15.6
libc6 >= 2.7
libgomp1 >= 4.4
zlib1g >= 1:1.2.6

Download

Type URL
Binary Package velvet_1.2.03~nozlibcopy-1_amd64.deb
Source Package velvet

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install velvet deb package:
    # sudo apt-get install velvet

Files

Path
/usr/bin/velvetg
/usr/bin/velvetg_de
/usr/bin/velveth
/usr/bin/velveth_de
/usr/share/doc-base/velvet
/usr/share/doc/velvet/CREDITS.txt
/usr/share/doc/velvet/Manual.pdf
/usr/share/doc/velvet/README.Debian
/usr/share/doc/velvet/README.txt
/usr/share/doc/velvet/changelog.Debian.gz
/usr/share/doc/velvet/changelog.gz
/usr/share/doc/velvet/copyright
/usr/share/man/man1/velvetg.1.gz
/usr/share/man/man1/velvetg_de.1.gz
/usr/share/man/man1/velveth.1.gz
/usr/share/man/man1/velveth_de.1.gz
/usr/share/velvet/shuffleSequences_fasta.pl
/usr/share/velvet/shuffleSequences_fastq.pl
/usr/share/velvet/contrib/README.txt
/usr/share/velvet/contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py
/usr/share/velvet/contrib/AssemblyAssembler1.3/README.txt
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/LICENSE.txt
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/Makefile
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/README.txt
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/scriptEstimatedCovMulti.py
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/shuffleAndConvertSequences_fastq2fasta.py
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/shuffleSequences_fasta.pl
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/shuffleSequences_fastq.pl
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/concatenatedGraph.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/concatenatedGraph.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/concatenatedPreGraph.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/concatenatedPreGraph.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/correctedGraph.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/correctedGraph.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/crc.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/crc.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/dfib.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/dfib.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/dfibHeap.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/dfibHeap.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/dfibpriv.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/fib.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/fib.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/fibHeap.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/fibHeap.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/fibpriv.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/globals.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/graph.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/graph.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/graphReConstruction.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/graphReConstruction.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/graphStats.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/graphStats.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/kmer.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/kmer.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/locallyCorrectedGraph.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/locallyCorrectedGraph.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/passageMarker.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/passageMarker.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/preGraph.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/preGraph.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/preGraphConstruction.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/preGraphConstruction.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/readCoherentGraph.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/readCoherentGraph.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/readSet.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/readSet.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/recycleBin.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/recycleBin.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/roadMap.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/roadMap.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/run.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/run.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/run2.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/scaffold.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/scaffold.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/sequenceExpander.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/sequenceExpander.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/shortReadPairs.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/shortReadPairs.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/splay.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/splay.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/splayTable.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/splayTable.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/tightString.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/tightString.h
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/tmp.ps
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/utility.c
/usr/share/velvet/contrib/MetaVelvet-v0.3.1/src/utility.h
/usr/share/velvet/contrib/VelvetOptimiser-2.2.0/README
/usr/share/velvet/contrib/VelvetOptimiser-2.2.0/VelvetOptimiser.pl
/usr/share/velvet/contrib/VelvetOptimiser-2.2.0/VelvetOpt/Assembly.pm
/usr/share/velvet/contrib/VelvetOptimiser-2.2.0/VelvetOpt/Utils.pm
/usr/share/velvet/contrib/VelvetOptimiser-2.2.0/VelvetOpt/gwrap.pm
/usr/share/velvet/contrib/VelvetOptimiser-2.2.0/VelvetOpt/hwrap.pm
/usr/share/velvet/contrib/afg_handling/asmbly_splitter.pl
/usr/share/velvet/contrib/afg_handling/snp_view.pl
/usr/share/velvet/contrib/columbus_scripts/enlarge_exons.pl
/usr/share/velvet/contrib/columbus_scripts/gff2fasta.pl
/usr/share/velvet/contrib/columbus_scripts/merge_gtf_exons.pl
/usr/share/velvet/contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl
/usr/share/velvet/contrib/extractContigReads/extractContigReads.pl
/usr/share/velvet/contrib/fasta2agp/fasta2agp.pl
/usr/share/velvet/contrib/observed-insert-length.pl/observed-insert-length.pl
/usr/share/velvet/contrib/select_paired/select_paired.pl
/usr/share/velvet/contrib/show_repeats/show_repeats.pl
/usr/share/velvet/contrib/shuffleSequences_fasta/kseq.h
/usr/share/velvet/contrib/shuffleSequences_fasta/shuffleSeqs-fast.c
/usr/share/velvet/contrib/shuffleSequences_fasta/shuffleSequences_fasta.pl
/usr/share/velvet/contrib/shuffleSequences_fasta/shuffleSequences_fasta.py
/usr/share/velvet/contrib/shuffleSequences_fasta/shuffleSequences_fasta.sh
/usr/share/velvet/contrib/solaris/recycleBin.c

Changelog

2012-02-16 - Charles Plessy <plessy@debian.org>
velvet (1.2.03~nozlibcopy-1) unstable; urgency=low
* New upstream release.
* Updated debian/patches/include_debians_zlib.patch.
2011-12-09 - Charles Plessy <plessy@debian.org>
velvet (1.1.07~nozlibcopy-1) unstable; urgency=low
* New upstream release (Closes: #647415).
* debian/contol:
- Pre-Depends on dpkg (>= 1.15.6) for Ubuntu LTS.
- Removed Multi-Arch: foreign.
2011-09-27 - Charles Plessy <plessy@debian.org>
velvet (1.1.06~nozlibcopy-1) unstable; urgency=low
[ Andreas Tille ]
* New upstream version
* debian/copyright: Revised
* debian/get-orig-source: Do not remove MetaVelvet
* debian/control:
Build-Depends: texlive-latex-base
[ Charles Plessy ]
* Corrected VCS URLs in debian/control.
* Compress source and binary packages with xz
(debian/rules, debian/get-orig-source).
* Turn on multithreading with OpenMP (debian/rules).
* Remove empty directory contrib/MetaVelvet-v0.3.1/obj (debian/rules).
2011-08-11 - Tim Booth <tbooth@ceh.ac.uk>
velvet (1.1.05-1ubuntu4) lucid; urgency=low
* Moved from CDBS to DH
* New upstream.  Still includes a copy of Zlib but the default
is now to use the system version, so removed relevant patch.
* Modified build to work on unmodified upstream (still works on
pruned upstream).
2011-04-15 - Andreas Tille <tille@debian.org>
velvet (1.1.02~nozlibcopy-1) unstable; urgency=low
* New upstream version
upgraded patches, tweak $(LIBS) into Z_LIB_FILES variable
of Makefile which makes patch more robust against upstream
changes
* Debhelper 8 (control+compat)
* debian/rules: Leave out Z_LIB_FILES in parameter list
* debian/get-orig-source: Once we are rebuilding the original
tarball anyway it makes sense to remove an outdated copy of
MetaVelvet and replace it rather by a hint to the currently
maintained source in README.source
* Standards-Version: 3.9.2 (no changes needed)
2011-01-19 - Andreas Tille <tille@debian.org>
velvet (1.0.18~nozlibcopy-1) unstable; urgency=low
* New upstream version
* debian/get-orig-source: Make sure MD5sum stays the same for different
download
2010-12-20 - Andreas Tille <tille@debian.org>
velvet (1.0.15~nozlibcopy-2) unstable; urgency=low
* Fix FTBFS with ld --as-needed (thanks for the patch to
Matthias Klose)
Closes: #607535
2010-11-24 - Andreas Tille <tille@debian.org>
velvet (1.0.15~nozlibcopy-1) unstable; urgency=low
* New upstream source
* Standards-Version: 3.9.1 (no changes needed)
* debian/get-upstream-source: Remove precompiled *.o files and
.DS_Store files once we are repackaging anyway
* debian/patches/fix-perl-path.patch: Fix Perl path
2010-06-24 - Andreas Tille <tille@debian.org>
velvet (1.0.02~nozlibcopy-1) unstable; urgency=low
* New upstream version
* Source format 3.0 (quilt)
* debian/control:
- Recommends: python (some new scripts in /usr/share/velvet/contrib
are Python scripts)
- Build-Depends: quilt
* debian/rules:
include /usr/share/cdbs/1/rules/patchsys-quilt.mk
(instead of simple-patchsys)
* debian/patches: Switch to quilt
* debian/patches/shuffleSequences_fasta.patch:
Add interpreter to Python script
2010-03-22 - Andreas Tille <tille@debian.org>
velvet (0.7.61~nozlibcopy-1) unstable; urgency=low
* New upstream version
* debian/get-orig-source, debian/rules: Strip zlib copy from
upstream tarball

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vflib3-doc_3.6.14.dfsg-3_all.deb Documentation for VFlib3
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